Post-translational modifications are intimately involved in regulation of the protein function in the cell. Detecting the presence of modifications on proteins and quantifying their abundance is a prerequisite for understanding their role in biological processes. Despite a certain success in using several techniques such as radiography, Edman sequencing and immunochemistry to reveal modifications, this study continues to present formidable analytical challenge. Mass spectrometry based methods are beginning to play an increasingly important role in this task. A linked scan mode of operation of several types of mass spectrometers exhibits an exceptional promise for detecting and profiling several types of modifications. The technique is highly selective and based on the coincidence of observing a particular characteristic fragment in the fragmentation spectrum of a compound. Presently, the efficiency of this mode reaches only a fraction of percent because of the precursor ion selection step during which all other ions are rejected linked scan analysis. The aim of this project is (1) to build a new type of mass spectrometer for collecting linked scan spectra with efficiency close to 100% and (2) to implement this mass spectrometer for detecting and profiling modification sites on proteins. The construction of the mass spectrometer is based on a novel high ion capacity linear ion trap combined in a tandem configuration with a quadrupole collision cell and a quadrupole mass analyzer. The novel linear ion trap can store a large number of ions without degradation in performance because of space charge effects. All ions stored in the ion trap can be sequentially fragmented in the collision cell during the ejection process, but only particular ion fragments can be transmitted to the detector through the quadrupole mass analyzer whose scan is linked to the ion trap ejection scan. Thus, a linked scan spectrum can be obtained from all ions stored in the ion trap during a single scan of the instrument resulting in 100-1000 fold increase in efficiency of the device. This mass spectrometer can be used to detect modification sites on proteins with an unprecedented speed and sensitivity. It will have an immense value for monitoring particular products in the complex mixtures and,ultimately, for collecting fragmentation spectra from all observed species. When built, it will quickly become an indispensable research tool for advancement the frontiers of the biomedical research.